Re: [galaxy-dev] apache on ubuntu

[Will Holtz]

You may need to load the mod_rewrite module. This can be done via:
sudo a2enmod rewrite

-Will

On Mon, Sep 5, 2016 at 7:10 AM, Raymond Wan  wrote:

> Hi Jochen,
>
>
>
> On Sat, Sep 3, 2016 at 2:31 AM, Bick  Jochen 
> wrote:
> > RewriteEngine on
> > RewriteRule ^(.*) http://localhost:8080$1 [P]
> ...
> > but it does not have any effect. Here the error.log but there is no
> error:
> > [Fri Sep 02 15:28:21.677881 2016] [mpm_event:notice] [pid 6627:tid
> 140049034254208] AH00493: SIGUSR1 received.  Doing graceful restart
>
> I presume you've restarted the web server after making this change?
>
> Apache's mod_rewrite (the module you are using to achieve the above)
> has a logging facility, which you might want to read about:
>
> http://httpd.apache.org/docs/current/mod/mod_rewrite.html#logging
>
> Also, as what you're trying to do isn't specific to Galaxy, you might
> want to ask your questions on other forums.  (i.e., askubuntu, etc.)
> They may not know what Galaxy is, but if you pose the problem as a
> redirection from port 80 to 8080 (and you wanted 443, as well?), I
> think an Apache expert (not me; I have gotten what you're doing
> working before, but it was a while ago and maybe I was just lucky) may
> be able to help.
>
> Ray
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Re: [galaxy-dev] apache on ubuntu

[Raymond Wan]

Hi Jochen,



On Sat, Sep 3, 2016 at 2:31 AM, Bick  Jochen  wrote:
> RewriteEngine on
> RewriteRule ^(.*) http://localhost:8080$1 [P]
...
> but it does not have any effect. Here the error.log but there is no error:
> [Fri Sep 02 15:28:21.677881 2016] [mpm_event:notice] [pid 6627:tid 
> 140049034254208] AH00493: SIGUSR1 received.  Doing graceful restart

I presume you've restarted the web server after making this change?

Apache's mod_rewrite (the module you are using to achieve the above)
has a logging facility, which you might want to read about:

http://httpd.apache.org/docs/current/mod/mod_rewrite.html#logging

Also, as what you're trying to do isn't specific to Galaxy, you might
want to ask your questions on other forums.  (i.e., askubuntu, etc.)
They may not know what Galaxy is, but if you pose the problem as a
redirection from port 80 to 8080 (and you wanted 443, as well?), I
think an Apache expert (not me; I have gotten what you're doing
working before, but it was a while ago and maybe I was just lucky) may
be able to help.

Ray
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[galaxy-dev] Galaxy Tools XSD - searching for help!

[Björn Grüning]

Dear community,

is there someone that is familiar with XSD files and validating XML files?
We need help in updating our Galaxy Tools XSD file:
https://github.com/galaxyproject/Galaxy-XSD/blob/master/galaxy.xsd

The idea is to auto generate documentation out of it and improve planemo
lint. If you have these skills please get in touch with us :)

Thanks!
Bjoern
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[galaxy-dev] display at UCSC does not work

[Hans-Rudolf Hotz]

Hi


I am trying to set up the possibility to display data sets with the UCSC 
genome browser for our new galaxy installation.


After clicking on "display at UCSC main", I get the UCSC genome browser, 
opening in the right assembly, and at the correct location, but I get 
the following Error:


Warning/Error(s):

redirected to non-http(s): /login?redirect=%2Froot%2Fdisplay_as



In galaxy.ini, I did uncomment the line:

display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse. ...


We use the 'new' authentication method to connect to our LDAP server, 
with the following changes in galaxy.ini:


require_login = True

auth_config_file = config/auth_conf.xml


Connection from UCSC to our galaxy server is working, since I can 
display the data, when I switch to


require_login = False

it works, independent of whether I am logged in or not.



Is there a way to get it to work, even if I have "require_login = True"?


Thank you very much for your help
Regards, Hans-Rudolf





--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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